Figure 1.
(A) Secondary structure and long-range tertiary contacts of the Tetrahymena group I ribozyme. P and L stand for base-paired and looped regions, respectively.15 The five long-range contacts are indicated by colored arrows and labeled with their names and with the fold decrease (colored numbers in parentheses) in the P1 docking equilibrium constant for the mutant compared to the wild type (WT) ribozyme (data from ref (6)). MC/MCR stands for metal core/metal core receptor.16 TL/TLR stands for tetraloop/tetraloop receptor.17 Regions that were mutated to remove the long-range contacts are colored; the name of the mutated sites and the substituted residues are depicted beside each mutation site. ARB stands for A-rich bulge.18 The site of cleavage is indicted by a black arrow. (B) The P1 docking process. P1 (red) is the duplex formed between the oligomer substrate (in lower case in part A) and the 5′-internal guide sequence (IGS in part A) of the ribozyme. P1 docks into the ribozyme’s conserved core where it forms tertiary interactions. (C) The chemical structure of 6-methyl isoxanthopterin (6-MI) used in the FPA measurements. See the Experimental section for the 6-MI-containing P1 sequence.